DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Nanopore sequence read simulator
Viral genomics analysis pipelines
A package for designing compact and comprehensive capture probe sets.
Genetic learning algorithm implementation for simulations, games, or general machine learning problems
Efficiently keep track of changes to genomes
Understand DNA structure and how machine learning can be used to work with DNA sequence data.
A tool for simulating random mutations in any genome
A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.
C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.
Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
A high performance tool to identify orthologs and paralogs across genomes.
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